OCA Atlas for 1BCC

1BCC

Oxidoreductase

date

Mar 23, 1998

title

Cytochrome Bc1 Complex From Chicken

authors

Z.Zhang, L.Huang, V.M.Shulmeister, Y.I.Chi, K.K.Kim, L.W.Hung, A.R.Crofts, E.A.Berry, S.H.Kim

compound

source

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: A
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
Organ: Heart
Tissue: Muscle
Organelle: Mitochondria
Cellular_location: Mitochondrial Inner Membrane
Other_details: Isolated From Natural Heart Muscle Tissue

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: B
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: C
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: D
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: E
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: F
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: G
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: H
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: I
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: J
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Includes Ubiquinone And Phospholipids

symmetry

Space Group: P 21 21 21

R_factor

0.270

R_Free

0.310

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
169.590	182.518	240.573	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.16 Å

ligand

BOG, FES, HEM, PEE, U10

enzyme

Oxidoreductase E.C.1.10.2.2 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A
B
C
D
E
F
G
H
J

Primary reference

Electron transfer by domain movement in cytochrome bc1., Zhang Z, Huang L, Shulmeister VM, Chi YI, Kim KK, Hung LW, Crofts AR, Berry EA, Kim SH, Nature 1998 Apr 16;392(6677):677-84. PMID:9565029

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (317 Kb) [Save to disk]

Biological Unit Coordinates (1bcc.pdb1.gz) 610 Kb

LPC: Ligand-Protein Contacts for 1BCC

CSU: Contacts of Structural Units for 1BCC

Likely Quarternary Molecular Structure file(s) for 1BCC

Structure Factors (1230 Kb)

Retrieve 1BCC in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1BCC from S2C, [Save to disk]

Re-refined 1bcc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1BCC in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1BCC

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1BCC, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1bcca2, region A:233-445 [Jmol] [rasmolscript] [script source]
- Domain d1bcca1, region A:4-232 [Jmol] [rasmolscript] [script source]
- Domain d1bccb1, region B:18-235 [Jmol] [rasmolscript] [script source]
- Domain d1bccb2, region B:236-439 [Jmol] [rasmolscript] [script source]
- Domain d1bccc3, region C:2-261 [Jmol] [rasmolscript] [script source]
- Domain d1bccc2, region C:262-380 [Jmol] [rasmolscript] [script source]
- Domain d1bccd2, region D:1-195 [Jmol] [rasmolscript] [script source]
- Domain d1bccd3, region D:196-241 [Jmol] [rasmolscript] [script source]
- Domain d1bcce2, region E:1-69 [Jmol] [rasmolscript] [script source]
- Domain d1bcce1, region E:70-196 [Jmol] [rasmolscript] [script source]
- Domain d1bccf_, region F [Jmol] [rasmolscript] [script source]
- Domain d1bccg_, region G [Jmol] [rasmolscript] [script source]
- Domain d1bcch_, region H [Jmol] [rasmolscript] [script source]
- Domain d1bccj_, region J [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1bcc_D] [1bcc_G] [1bcc_B] [1bcc_J] [1bcc_A] [1bcc] [1bcc_F] [1bcc_E] [1bcc_H] [1bcc_I] [1bcc_C]

SWISS-PROT database: [P00125] [P18946] [P31800] [P23004] [P00126] [P00129] [P13271] [P00130] [P13272]

Belongs to the proton-translocating quinol:cytochrome c reductase (qcr) superfamily

according to TCDB.

Domain organization of [CY1_BOVIN] [CYB_CHICK] [QCR1_BOVIN] [QCR2_BOVIN] [QCR6_BOVIN] [QCR7_BOVIN] [QCR8_BOVIN] [QCR9_BOVIN] [UCRI_BOVIN] by SWISSPFAM

Other resources with information on 1BCC

Community annotation for 1BCC at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1BCC from the Database of Macromolecular Movements.

Images from IMB Jena Image Library of Biological Macromolecules.

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